The University of California, Santa Cruz (UCSC) Genome Browser (1,2) is a web-based resource for the biomedical community, providing timely and convenient access to sequence and annotations for human and other vertebrate reference species genomes, along with selected model invertebrates. The minimal set of annotation ‘tracks’ on every browser generally includes assembly and gaps, the percentage of guanine and cytosine bases, alignments of RefSeq genes (3,4), mRNAs and ESTs obtained from GenBank (5) and repeat region annotations. Most browsers also include one or more gene or gene prediction tracks, including Ensembl Genes (6), as well as comparative genomics tracks that show pairwise genomic sequence alignments (chain and net tracks) between organisms. About half of the organisms hosted in the browser include multiple sequence alignment (multiz) tracks (7). The human and mouse browsers feature a gene prediction track created at UCSC—UCSC Genes (2,8,9)—based on data from RefSeq, GenBank, CCDS and UniProt. Many more expression, regulation, variation and phenotype tracks are available on the model organism and human browsers.
